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analyze_gc
Martin Asser Hansen edited this page Oct 2, 2015
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analyze_gc analyzes the sequence specified by the SEQ key in each record and adds a
GC% key with the percentage GC composition of that particular sequence.
For more complex sequence analysis use analyze_seq.
... | analyze_gc [options]
[-? | --help] # Print full usage description.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the file test.fna containing the single entry:
>test
ACGACGCATNNNNNNactgatcga
To analyze this sequence, read the file using read_fasta:
SEQ_NAME: test
GC%: 37.50
SEQ: ACGACGCATNNNNNNactgatcga
SEQ_LEN: 24
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If you have a stack of sequences in one file and you want to determine the mean GC content of all the sequences, you can do it using the mean_vals biopiece:
read_fasta -i test.fna | analyze_gc | mean_vals -k GC% -x
GC%_MEAN: 37.50
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Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
analyze_gc is part of the Biopieces framework.